def test_parse_header(medium_header):
p = parser.Parser(stream=medium_header, path="<builtin>")
header = p.parse_header()
assert header.lines
assert len(header.lines) == 18
EXPECTED = "HeaderLine('fileformat', 'VCFv4.3')"
assert str(header.lines[0]) == EXPECTED
if sys.version_info < (3, 6):
EXPECTED = (
"FormatHeaderLine('FORMAT', '<ID=HQ,Number=2,Type=Integer,"
"Description=\"Haplotype Quality\">', OrderedDict([('ID', 'HQ'), "
"('Number', 2), ('Type', 'Integer'), ('Description', "
"'Haplotype Quality')]))")
else:
EXPECTED = (
"FormatHeaderLine('FORMAT', '<ID=HQ,Number=2,Type=Integer,Description=\"Haplotype Quality\">', "
"{'ID': 'HQ', 'Number': 2, 'Type': 'Integer', 'Description': 'Haplotype Quality'})"
)
assert str(header.lines[-1]) == EXPECTED
assert header.samples.names == ["NA00001", "NA00002", "NA00003"]
def vcf_parser(lines):
return parser.Parser(io.StringIO(MEDIUM_HEADER + lines), "<builtin>")
def vcf_header():
p = parser.Parser(io.StringIO(HEADER))
return p.parse_header()
def header_samples():
p = parser.Parser(stream=io.StringIO(MEDIUM_HEADER), path="<builtin>")
p.parse_header()
return (p.header, p.samples)